Asymmetric adapter library construction

ABSTRACT

The present invention provides methods and compositions for asymmetrically tagging a nucleic acid fragment using asymmetric adapters.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.12/432,080 filed Apr. 29, 2009, now U.S. Pat. No. 8,029,993, whichclaims the benefit under 35 U.S.C. §119(e) of U.S. ProvisionalApplication Ser. No. 61/049,323 filed Apr. 30, 2008, both of which areincorporated herein by reference.

BACKGROUND

Numerous nucleic acid analysis processes require or are greatlyfacilitated by asymmetrically labeling the nucleic acids under study.For example, asymmetric tagging allows one to control subsequentmanipulations and reactions with respect to one particular strand of DNA(e.g., Crick vs. Watson). One method of achieving asymmetric tagging ofa nucleic acid employs DNA strand methylation by the enzyme Dammethylase (see, e.g., U.S. Pat. No. 7,217,522 and provisional U.S.Patent application 60/947,109, filed on Jun. 29, 2007, both of which areincorporated by reference herein). Alternatively, one can incorporate 5methyl-dCTP during strand replication rather than employing Dammethylase to achieve a similar result. Another method employs variousbiotin labeling and pullout tricks to isolate asymmetrically labeledfragments (see, e.g., Nature vol. 437, p 376-380 (2005)).

Given the incredible expansion of nucleic acid-based assays (e.g., inthe field of comparative genomics), there is a significant demand formethods that can simplify nucleic acid manipulation and analysis.

SUMMARY OF THE INVENTION

The present invention provides methods and compositions forasymmetrically tagging a nucleic acid fragment using asymmetricadapters.

Aspects of the present invention include methods of producing anasymmetrically tagged nucleic acid fragment including the steps of: i)ligating an adapter to each end of a double-stranded nucleic acidfragment, wherein the adapter includes: (a) a first and a second nucleicacid strand associated with each other via one or more complementarydomains, the adapter having a first end and a second end; (b) one ormore region of substantial non-complementarity between the first andsecond nucleic acid strands; (c) a ligation site positioned on the firstend of the adapter configured to allow ligation of the adapter to thedouble stranded nucleic acid fragment; and (d) a hairpin structurepositioned on the 3′ strand on the second end of the adaptor, thehairpin structure producing a nucleic acid synthesis self-priming site;and ii) performing a first round of nucleic acid synthesis initiatedfrom the self-priming site, thereby producing an asymmetrically taggednucleic acid fragment.

In certain embodiments, the nucleotide polymerase used in the nucleicacid synthesis is selected from the group consisting of: a RNApolymerase, a mesophilic DNA polymerase, a reverse transcriptase, and athermophilic DNA polymerase.

In certain embodiments, the region of substantial non-complementarity,the first and/or second nucleic acid strands include one or more of thefollowing: a unique identifier (UID), an RNA polymerase promoter region,a primer binding site, a restriction enzyme site, and a recombinationsite.

In certain embodiments, the adaptor includes an RNA polymerase promoterregion adjacent to the hairpin structure or within the duplex region ofthe hairpin structure.

In certain embodiments, the RNA promoter region is oriented such thatRNA polymerization proceeds toward the hairpin structure.

In certain embodiments, the double-stranded nucleic acid fragment isproduced by digesting a parent double-stranded nucleic acid sample witha restriction enzyme and polishing the ends of the resultant restrictionenzyme fragments to create ends compatible with the ligation site of theadapter.

In certain embodiments, the method further includes isolating one strandof the asymmetrically tagged nucleic acid fragment.

In certain embodiments, the isolating includes treating theasymmetrically tagged nucleic acid fragment with an exonuclease selectedto digest only one strand of the asymmetrically tagged nucleic acidfragment.

Aspects of the subject invention include nucleic acid adaptersincluding: (a) a first and a second nucleic acid strand associated witheach other via one or more complementary domains, the adapter having afirst end and a second end; (b) one or more region of substantialnon-complementarity between the first and second nucleic acid strands;(c) a ligation site positioned on the first end of the adapterconfigured to allow ligation of the adapter to a double stranded nucleicacid fragment; and (d) a hairpin structure positioned on the 3′ strandon the second end of the adaptor, the hairpin structure producing anucleic acid synthesis self-priming site.

In certain embodiments, the region of substantial non-complementarity inthe first or second nucleic acid strand includes one or more of thefollowing: a unique identifier (UID), an RNA polymerase promoter region,a primer binding site, a restriction enzyme site, and a recombinationsite.

In certain embodiments, the adaptor includes an RNA polymerase promoterregion adjacent to the hairpin structure or within the duplex region ofthe hairpin structure.

Aspects of the present invention include methods of producing anasymmetrically tagged nucleic acid fragment, the method including: i)ligating an adapter to both ends of a double-stranded nucleic acidfragment, wherein the adapter includes: (a) a first and a second nucleicacid strand hybridized together, wherein the hybridized strands includeone or more wobble base pair; (b) a ligation site positioned on a firstend of the hybridized strands configured to allow ligation of theadapter to the double stranded nucleic acid fragment; and (c) a nucleicacid synthesis primer binding site positioned upstream of the one ormore wobble base pair; ii) annealing a synthesis primer specific for thenucleic acid synthesis primer binding site to the adaptor ligatedfragment; and iii) performing a first round of nucleic acid synthesisinitiated from the annealed synthesis primer, wherein the nucleotidebase incorporated at the one or more wobble base pair in the adapterregion at a first end of the adaptor ligated fragment is different thanthe corresponding nucleotide in the adapter region at a second end ofthe adapter ligated fragment, thereby producing an asymmetrically taggednucleic acid fragment.

In certain embodiments, the one or more wobble base pair is positionedwithin the adapter such that the resultant asymmetrically tagged nucleicacid fragment includes a restriction enzyme recognition and/or cut siteat only one end.

In certain embodiments, the one or more wobble base pair is positionedwithin the ligation site.

In certain embodiments, the method further includes: digesting theasymmetrically tagged nucleic acid fragment with a restriction enzymespecific for the restriction enzyme recognition and/or cut site; andligating a second, different adapter to the digested fragment, thesecond adapter having a ligation site compatible with the digested endof the fragment.

In certain embodiments, the method further includes isolating one strandof the asymmetrically tagged nucleic acid fragment.

In certain embodiments, the isolating includes treating theasymmetrically tagged nucleic acid fragment with an exonuclease selectedto digest only one strand of the asymmetrically tagged nucleic acidfragment.

In certain embodiments, the adapter further includes one or more of thefollowing: a unique identifier (UID), an RNA polymerase promoter region,a primer binding site, a restriction enzyme site, and a recombinationsite.

Aspects of the present invention include an adapter including: (a) afirst and a second nucleic acid strand hybridized together, wherein thehybridized strands include one or more wobble base pair; (b) a ligationsite positioned on a first end of the adapter configured to allowligation of the adapter to a compatible end of a double stranded nucleicacid fragment; and (c) a nucleic acid synthesis primer binding sitepositioned upstream of the one or more wobble base pair.

In certain embodiments, the one or more wobble base pair is positionedwithin a restriction enzyme recognition and/or cut site in the adapter.

In certain embodiments, the adapter further includes one or more of thefollowing: a unique identifier (UID), an RNA polymerase promoter region,a primer binding site, a restriction enzyme site, and a recombinationsite.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is best understood from the following detailed descriptionwhen read in conjunction with the accompanying drawings. It isemphasized that, according to common practice, the various features ofthe drawings are not to-scale. Indeed, the dimensions of the variousfeatures are arbitrarily expanded or reduced for clarity. Included inthe drawings are the following figures:

FIGS. 1A, 1B and 1C show exemplary structural components of asymmetricadapters that find use in practicing aspects of the subject invention.

FIG. 2 shows the sequence, secondary structure and domains of a specificexample of an asymmetric adapter that finds use in practicing aspects ofthe subject invention.

FIG. 3 shows an exemplary embodiment of producing asymmetrically taggednucleic acid fragments according to aspects of the subject invention.

FIG. 4 shows an exemplary embodiment of an asymmetrically tagged genomicfragment (GF) in which the adapter contains specific elements.

FIG. 5 shows another exemplary embodiment of an asymmetric adapteraccording to aspects of the present invention. This adapter is similarto the “Y” adapter as shown in FIG. 1A but includes a hairpin structureon the 3′ end of the asymmetric region.

FIG. 6 shows exemplary embodiments of asymmetric adapters with wobblebases. A and B show how wobble bases produce asymmetrically taggedfragments after replication. C and D show how wobble bases can beemployed to generate fragments having asymmetrically positionedrestriction enzyme sites.

FIG. 7 shows an exemplary embodiment of an adapter having wobble basespositioned within the ligation site of the adapter followed by ligationof a second, different adapter.

FIG. 8 shows the asymmetric adapter sequence (SEQ ID NO: 1 and SEQ IDNO: 2) and its domain structure as employed in Example 1. This specificasymmetric adapter is designed to be ligated to nucleic acid fragmentshaving a 5′ GATC overhang filled-in with dGTP. Also shown are sequencesfor the reverse primer (SEQ ID NO: 3) and T3 promoter primer (SEQ ID NO:4), the use of which are described in detail in the Examples sectionbelow.

FIG. 9 shows secondary structure of the asymmetric adapter shown in FIG.8.

FIG. 10 shows results of experiments analyzing the structure of theasymmetric adapter shown in FIG. 8 using single stranded DNA specificexonuclease Exonuclease I and/or double stranded specific exonucleaselambda exonuclease.

FIG. 11 shows construction of a asymmetric adapter library from lambdaDNA digested with BstYI.

FIG. 12 shows the pattern of in vitro transcription (IVT) reaction usingthe adapter library in FIG. 11 as a template.

FIG. 13 shows 1st strand cDNA synthesis from the transcripts produced inFIG. 12.

FIG. 14 shows sequencing gel analysis of synthesized first strand cDNAproduced from RNA derived from IVT of asymmetrically tagged nucleic acidfragments.

FIG. 15 shows an asymmetric adapter ligated nucleic acid fragment havingan annealed primer that forms a T3 RNA polymerase promoter useful in IVTreactions.

FIGS. 16A, 16B and 16C show extension products of an exemplaryasymmetric adapter ligated nucleic acid fragment. 16A shows DNApolymerase extension using the bottom strand as a template and the T3promoter primer 502. The T3 promoter site is indicated in box 510. 16Bshows DNA polymerase extension using the top strand produced in 16A as atemplate and a reverse primer 512. 16C shows T3 RNA polymerase IVTextension using double stranded T3 promoter site 510 as shown in 16A(and in FIG. 15), followed by reverse transcriptase extension in theopposite direction using reverse primer 512.

DEFINITIONS

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Still, certain elements aredefined for the sake of clarity and ease of reference.

Terms and symbols of nucleic acid chemistry, biochemistry, genetics, andmolecular biology used herein follow those of standard treatises andtexts in the field, e.g. Kornberg and Baker, DNA Replication, SecondEdition (W.H. Freeman, New York, 1992); Lehninger, Biochemistry, SecondEdition (Worth Publishers, New York, 1975); Strachan and Read, HumanMolecular Genetics, Second Edition (Wiley-Liss, New York, 1999);Eckstein, editor, Oligonucleotides and Analogs: A Practical Approach(Oxford University Press, New York, 1991); Gait, editor, OligonucleotideSynthesis: A Practical Approach (IRL Press, Oxford, 1984); and the like.

“Amplicon” means the product of a polynucleotide amplification reaction.That is, it is a population of polynucleotides, usually double stranded,that are replicated from one or more starting sequences. The one or morestarting sequences may be one or more copies of the same sequence, or itmay be a mixture of different sequences. Amplicons may be produced by avariety of amplification reactions whose products are multiplereplicates of one or more target nucleic acids. Generally, amplificationreactions producing amplicons are “template-driven” in that base pairingof reactants, either nucleotides or oligonucleotides, have complementsin a template polynucleotide that are required for the creation ofreaction products. In one aspect, template-driven reactions are primerextensions with a nucleic acid polymerase or oligonucleotide ligationswith a nucleic acid ligase. Such reactions include, but are not limitedto, polymerase chain reactions (PCRs), linear polymerase reactions,nucleic acid sequence-based amplification (NASBAs), rolling circleamplifications, and the like, disclosed in the following references thatare incorporated herein by reference: Mullis et al, U.S. Pat. Nos.4,683,195; 4,965,188; 4,683,202; 4,800,159 (PCR); Gelfand et al, U.S.Pat. No. 5,210,015 (real-time PCR with “TAQMAN™” probes); Wittwer et al,U.S. Pat. No. 6,174,670; Kacian et al, U.S. Pat. No. 5,399,491(“NASBA”); Lizardi, U.S. Pat. No. 5,854,033; Aono et al, Japanese patentpubl. JP 4-262799 (rolling circle amplification); and the like. In oneaspect, amplicons of the invention are produced by PCRs. Anamplification reaction may be a “real-time” amplification if a detectionchemistry is available that permits a reaction product to be measured asthe amplification reaction progresses, e.g. “real-time PCR” describedbelow, or “real-time NASBA” as described in Leone et al, Nucleic AcidsResearch, 26: 2150-2155 (1998), and like references. As used herein, theterm “amplifying” means performing an amplification reaction. A“reaction mixture” means a solution containing all the necessaryreactants for performing a reaction, which may include, but not belimited to, buffering agents to maintain pH at a selected level during areaction, salts, co-factors, scavengers, and the like.

The term “assessing” includes any form of measurement, and includesdetermining if an element is present or not. The terms “determining”,“measuring”, “evaluating”, “assessing” and “assaying” are usedinterchangeably and includes quantitative and qualitativedeterminations. Assessing may be relative or absolute. “Assessing thepresence of” includes determining the amount of something present,and/or determining whether it is present or absent. As used herein, theterms “determining,” “measuring,” and “assessing,” and “assaying” areused interchangeably and include both quantitative and qualitativedeterminations.

“Complementary” or “substantially complementary” refers to thehybridization or base pairing or the formation of a duplex betweennucleotides or nucleic acids, such as, for instance, between the twostrands of a double stranded DNA molecule or between an oligonucleotideprimer and a primer binding site on a single stranded nucleic acid.Complementary nucleotides are, generally, A and T (or A and U), or C andG. Two single stranded RNA or DNA molecules are said to be substantiallycomplementary when the nucleotides of one strand, optimally aligned andcompared and with appropriate nucleotide insertions or deletions, pairwith at least about 80% of the nucleotides of the other strand, usuallyat least about 90% to 95%, and more preferably from about 98 to 100%.Alternatively, substantial complementarity exists when an RNA or DNAstrand will hybridize under selective hybridization conditions to itscomplement. Typically, selective hybridization will occur when there isat least about 65% complementary over a stretch of at least 14 to 25nucleotides, preferably at least about 75%, more preferably at leastabout 90% complementary. See, M. Kanehisa Nucleic Acids Res. 12:203(1984), incorporated herein by reference.

“Duplex” means at least two oligonucleotides and/or polynucleotides thatare fully or partially complementary undergo Watson-Crick type basepairing among all or most of their nucleotides so that a stable complexis formed. The terms “annealing” and “hybridization” are usedinterchangeably to mean the formation of a stable duplex. “Perfectlymatched” in reference to a duplex means that the poly- oroligonucleotide strands making up the duplex form a double strandedstructure with one another such that every nucleotide in each strandundergoes Watson-Crick base pairing with a nucleotide in the otherstrand. A stable duplex can include Watson-Crick base pairing and/ornon-Watson-Crick base pairing between the strands of the duplex (wherebase pairing means the forming hydrogen bonds). In certain embodiments,a non-Watson-Crick base pair includes a nucleoside analog, such asdeoxyinosine, 2,6-diaminopurine, PNAs, LNA's and the like. In certainembodiments, a non-Watson-Crick base pair includes a “wobble base”, suchas deoxyinosine, 8-oxo-dA, 8-oxo-dG and the like, where by “wobble base”is meant a nucleic acid base that can base pair with a first nucleotidebase in a complementary nucleic acid strand but that, when employed as atemplate strand for nucleic acid synthesis, leads to the incorporationof a second, different nucleotide base into the synthesizing strand(wobble bases are described in further detail below). A “mismatch” in aduplex between two oligonucleotides or polynucleotides means that a pairof nucleotides in the duplex fails to undergo Watson-Crick bonding.

“Genetic locus,” “locus,” or “locus of interest” in reference to agenome or target polynucleotide, means a contiguous sub-region orsegment of the genome or target polynucleotide. As used herein, geneticlocus, locus, or locus of interest may refer to the position of anucleotide, a gene or a portion of a gene in a genome, includingmitochondrial DNA or other non-chromosomal DNA (e.g., bacterialplasmid), or it may refer to any contiguous portion of genomic sequencewhether or not it is within, or associated with, a gene. A geneticlocus, locus, or locus of interest can be from a single nucleotide to asegment of a few hundred or a few thousand nucleotides in length ormore. In general, a locus of interest will have a reference sequenceassociated with it (see description of “reference sequence” below).

“Kit” refers to any delivery system for delivering materials or reagentsfor carrying out a method of the invention. In the context of reactionassays, such delivery systems include systems that allow for thestorage, transport, or delivery of reaction reagents (e.g., probes,enzymes, etc. in the appropriate containers) and/or supporting materials(e.g., buffers, written instructions for performing the assay etc.) fromone location to another. For example, kits include one or moreenclosures (e.g., boxes) containing the relevant reaction reagentsand/or supporting materials. Such contents may be delivered to theintended recipient together or separately. For example, a firstcontainer may contain an enzyme for use in an assay, while a secondcontainer contains probes.

“Ligation” means to form a covalent bond or linkage between the terminiof two or more nucleic acids, e.g. oligonucleotides and/orpolynucleotides, in a template-driven reaction. The nature of the bondor linkage may vary widely and the ligation may be carried outenzymatically or chemically. As used herein, ligations are usuallycarried out enzymatically to form a phosphodiester linkage between a 5′carbon of a terminal nucleotide of one oligonucleotide with 3′ carbon ofanother oligonucleotide. A variety of template-driven ligation reactionsare described in the following references, which are incorporated byreference: Whiteley et al, U.S. Pat. No. 4,883,750; Letsinger et al,U.S. Pat. No. 5,476,930; Fung et al, U.S. Pat. No. 5,593,826; Kool, U.S.Pat. No. 5,426,180; Landegren et al, U.S. Pat. No. 5,871,921; Xu andKool, Nucleic Acids Research, 27: 875-881 (1999); Higgins et al, Methodsin Enzymology, 68: 50-71 (1979); Engler et al, The Enzymes, 15: 3-29(1982); and Namsaraev, U.S. patent publication 2004/0110213.

“Nucleoside” as used herein includes the natural nucleosides, includingT-deoxy and 2′-hydroxyl forms, e.g. as described in Kornberg and Baker,DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992). “Analogs” inreference to nucleosides includes synthetic nucleosides having modifiedbase moieties and/or modified sugar moieties, e.g. described by Scheit,Nucleotide Analogs (John Wiley, New York, 1980); Uhlman and Peyman,Chemical Reviews, 90: 543-584 (1990), or the like, with the proviso thatthey are capable of specific hybridization. Such analogs includesynthetic nucleosides designed to enhance binding properties, reducecomplexity, increase specificity, and the like. Polynucleotidescomprising analogs with enhanced hybridization or nuclease resistanceproperties are described in Uhlman and Peyman (cited above); Crooke etal, Exp. Opin. Ther. Patents, 6: 855-870 (1996); Mesmaeker et al,Current Opinion in Structural Biology, 5: 343-355 (1995); and the like.Exemplary types of polynucleotides that are capable of enhancing duplexstability include oligonucleotide N3′→P5′ phosphoramidates (referred toherein as “amidates”), peptide nucleic acids (referred to herein as“PNAs”), oligo-2′-O-alkylribonucleotides, polynucleotides containing C-5propynylpyrimidines, locked nucleic acids (“LNAs”), and like compounds.Such oligonucleotides are either available commercially or may besynthesized using methods described in the literature.

“Polymerase chain reaction,” or “PCR,” means a reaction for the in vitroamplification of specific DNA sequences by the simultaneous primerextension of complementary strands of DNA. In other words, PCR is areaction for making multiple copies or replicates of a target nucleicacid flanked by primer binding sites, such reaction comprising one ormore repetitions of the following steps: (i) denaturing the targetnucleic acid, (ii) annealing primers to the primer binding sites, and(iii) extending the primers by a nucleic acid polymerase in the presenceof nucleoside triphosphates. Usually, the reaction is cycled throughdifferent temperatures optimized for each step in a thermal cyclerinstrument. Particular temperatures, durations at each step, and ratesof change between steps depend on many factors well-known to those ofordinary skill in the art, e.g. exemplified by the references: McPhersonet al, editors, PCR: A Practical Approach and PCR2: A Practical Approach(IRL Press, Oxford, 1991 and 1995, respectively). For example, in aconventional PCR using Taq DNA polymerase, a double stranded targetnucleic acid may be denatured at a temperature >90° C., primers annealedat a temperature in the range 50-75° C., and primers extended at atemperature in the range 72-78° C. The term “PCR” encompasses derivativeforms of the reaction, including but not limited to, RT-PCR, real-timePCR, nested PCR, quantitative PCR, multiplexed PCR, and the like.Reaction volumes range from a few hundred nanoliters, e.g. 200 mL, to afew hundred e.g. 200 μL. “Reverse transcription PCR,” or “RT-PCR,” meansa PCR that is preceded by a reverse transcription reaction that convertsa target RNA to a complementary single stranded DNA, which is thenamplified, e.g. Tecott et al, U.S. Pat. No. 5,168,038, which patent isincorporated herein by reference. “Real-time PCR” means a PCR for whichthe amount of reaction product, i.e. amplicon, is monitored as thereaction proceeds. There are many forms of real-time PCR that differmainly in the detection chemistries used for monitoring the reactionproduct, e.g. Gelfand et al, U.S. Pat. No. 5,210,015 (“TAQMAN™”);Wittwer et al, U.S. Pat. Nos. 6,174,670 and 6,569,627 (intercalatingdyes); Tyagi et al, U.S. Pat. No. 5,925,517 (molecular beacons); whichpatents are incorporated herein by reference. Detection chemistries forreal-time PCR are reviewed in Mackay et al, Nucleic Acids Research, 30:1292-1305 (2002), which is also incorporated herein by reference.“Nested PCR” means a two-stage PCR wherein the amplicon of a first PCRbecomes the sample for a second PCR using a new set of primers, at leastone of which binds to an interior location of the first amplicon. Asused herein, “initial primers” in reference to a nested amplificationreaction mean the primers used to generate a first amplicon, and“secondary primers” mean the one or more primers used to generate asecond, or nested, amplicon. “Multiplexed PCR” means a PCR whereinmultiple target sequences (or a single target sequence and one or morereference sequences) are simultaneously carried out in the same reactionmixture, e.g. Bernard et al, Anal. Biochem., 273: 221-228 (1999)(two-color real-time PCR). Usually, distinct sets of primers areemployed for each sequence being amplified.

“Quantitative PCR” means a PCR designed to measure the abundance of oneor more specific target sequences in a sample or specimen. QuantitativePCR includes both absolute quantitation and relative quantitation ofsuch target sequences. Quantitative measurements are made using one ormore reference sequences that may be assayed separately or together witha target sequence. The reference sequence may be endogenous or exogenousto a sample or specimen, and in the latter case, may comprise one ormore competitor templates. Typical endogenous reference sequencesinclude segments of transcripts of the following genes: β-actin, GAPDH,β₂-microglobulin, ribosomal RNA, and the like. Techniques forquantitative PCR are well-known to those of ordinary skill in the art,as exemplified in the following references that are incorporated byreference: Freeman et al, Biotechniques, 26: 112-126 (1999);Becker-Andre et al, Nucleic Acids Research, 17: 9437-9447 (1989);Zimmerman et al, Biotechniques, 21: 268-279 (1996); Diviacco et al,Gene, 122: 3013-3020 (1992); Becker-Andre et al, Nucleic Acids Research,17: 9437-9446 (1989); and the like.

“Polynucleotide” or “oligonucleotide” is used interchangeably and eachmean a linear polymer of nucleotide monomers. Monomers making uppolynucleotides and oligonucleotides are capable of specifically bindingto a natural polynucleotide by way of a regular pattern ofmonomer-to-monomer interactions, such as Watson-Crick type of basepairing, base stacking, Hoogsteen or reverse Hoogsteen types of basepairing, wobble base pairing, or the like. As described in detail below,by “wobble base” is meant a nucleic acid base that can base pair with afirst nucleotide base in a complementary nucleic acid strand but that,when employed as a template strand for nucleic acid synthesis, leads tothe incorporation of a second, different nucleotide base into thesynthesizing strand. Such monomers and their internucleosidic linkagesmay be naturally occurring or may be analogs thereof, e.g. naturallyoccurring or non-naturally occurring analogs. Non-naturally occurringanalogs may include peptide nucleic acids (PNAs, e.g., as described inU.S. Pat. No. 5,539,082, incorporated herein by reference), lockednucleic acids (LNAs, e.g., as described in U.S. Pat. No. 6,670,461,incorporated herein by reference), phosphorothioate internucleosidiclinkages, bases containing linking groups permitting the attachment oflabels, such as fluorophores, or haptens, and the like. Whenever the useof an oligonucleotide or polynucleotide requires enzymatic processing,such as extension by a polymerase, ligation by a ligase, or the like,one of ordinary skill would understand that oligonucleotides orpolynucleotides in those instances would not contain certain analogs ofinternucleosidic linkages, sugar moieties, or bases at any or somepositions. Polynucleotides typically range in size from a few monomericunits, e.g. 5-40, when they are usually referred to as“oligonucleotides,” to several thousand monomeric units. Whenever apolynucleotide or oligonucleotide is represented by a sequence ofletters (upper or lower case), such as “ATGCCTG,” it will be understoodthat the nucleotides are in 5′→3′ order from left to right and that “A”denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotesdeoxyguanosine, and “T” denotes thymidine, “I” denotes deoxyinosine, “U”denotes uridine, unless otherwise indicated or obvious from context.Unless otherwise noted the terminology and atom numbering conventionswill follow those disclosed in Strachan and Read, Human MolecularGenetics 2 (Wiley-Liss, New York, 1999). Usually polynucleotidescomprise the four natural nucleosides (e.g. deoxyadenosine,deoxycytidine, deoxyguanosine, deoxythymidine for DNA or their ribosecounterparts for RNA) linked by phosphodiester linkages; however, theymay also comprise non-natural nucleotide analogs, e.g. includingmodified bases, sugars, or internucleosidic linkages. It is clear tothose skilled in the art that where an enzyme has specificoligonucleotide or polynucleotide substrate requirements for activity,e.g. single stranded DNA, RNA/DNA duplex, or the like, then selection ofappropriate composition for the oligonucleotide or polynucleotidesubstrates is well within the knowledge of one of ordinary skill,especially with guidance from treatises, such as Sambrook et al,Molecular Cloning, Second Edition (Cold Spring Harbor Laboratory, NewYork, 1989), and like references.

“Primer” means an oligonucleotide, either natural or synthetic, that iscapable, upon forming a duplex with a polynucleotide template, of actingas a point of initiation of nucleic acid synthesis and being extendedfrom its 3′ end along the template so that an extended duplex is formed.The sequence of nucleotides added during the extension process isdetermined by the sequence of the template polynucleotide. Usuallyprimers are extended by a DNA polymerase. Primers are generally of alength compatible with its use in synthesis of primer extensionproducts, and are usually are in the range of between 8 to 100nucleotides in length, such as 10 to 75, 15 to 60, 15 to 40, 18 to 30,20 to 40, 21 to 50, 22 to 45, 25 to 40, and so on, more typically in therange of between 18-40, 20-35, 21-30 nucleotides long, and any lengthbetween the stated ranges. Typical primers can be in the range ofbetween 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-25 andso on, and any length between the stated ranges. In some embodiments,the primers are usually not more than about 10, 12, 15, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70nucleotides in length.

Primers are usually single-stranded for maximum efficiency inamplification, but may alternatively be double-stranded. Ifdouble-stranded, the primer is usually first treated to separate itsstrands before being used to prepare extension products. Thisdenaturation step is typically affected by heat, but may alternativelybe carried out using alkali, followed by neutralization. Thus, a“primer” is complementary to a template, and complexes by hydrogenbonding or hybridization with the template to give a primer/templatecomplex for initiation of synthesis by a polymerase, which is extendedby the addition of covalently bonded bases linked at its 3′ endcomplementary to the template in the process of DNA synthesis.

A “primer pair” as used herein refers to first and second primers havingnucleic acid sequence suitable for nucleic acid-based amplification of atarget nucleic acid. Such primer pairs generally include a first primerhaving a sequence that is the same or similar to that of a first portionof a target nucleic acid, and a second primer having a sequence that iscomplementary to a second portion of a target nucleic acid to providefor amplification of the target nucleic acid or a fragment thereof.Reference to “first” and “second” primers herein is arbitrary, unlessspecifically indicated otherwise. For example, the first primer can bedesigned as a “forward primer” (which initiates nucleic acid synthesisfrom a 5′ end of the target nucleic acid) or as a “reverse primer”(which initiates nucleic acid synthesis from a 5′ end of the extensionproduct produced from synthesis initiated from the forward primer).Likewise, the second primer can be designed as a forward primer or areverse primer.

“Readout” means a parameter, or parameters, which are measured and/ordetected that can be converted to a number or value. In some contexts,readout may refer to an actual numerical representation of suchcollected or recorded data. For example, a readout of fluorescentintensity signals from a microarray is the address and fluorescenceintensity of a signal being generated at each hybridization site of themicroarray; thus, such a readout may be registered or stored in variousways, for example, as an image of the microarray, as a table of numbers,or the like.

“Solid support”, “support”, and “solid phase support” are usedinterchangeably and refer to a material or group of materials having arigid or semi-rigid surface or surfaces. In many embodiments, at leastone surface of the solid support will be substantially flat, although insome embodiments it may be desirable to physically separate synthesisregions for different compounds with, for example, wells, raisedregions, pins, etched trenches, or the like. According to otherembodiments, the solid support(s) will take the form of beads, resins,gels, microspheres, or other geometric configurations. Microarraysusually comprise at least one planar solid phase support, such as aglass microscope slide.

“Specific” or “specificity” in reference to the binding of one moleculeto another molecule, such as a labeled target sequence for a probe,means the recognition, contact, and formation of a stable complexbetween the two molecules, together with substantially less recognition,contact, or complex formation of that molecule with other molecules. Inone aspect, “specific” in reference to the binding of a first moleculeto a second molecule means that to the extent the first moleculerecognizes and forms a complex with another molecule in a reaction orsample, it forms the largest number of the complexes with the secondmolecule. Preferably, this largest number is at least fifty percent.Generally, molecules involved in a specific binding event have areas ontheir surfaces or in cavities giving rise to specific recognitionbetween the molecules binding to each other. Examples of specificbinding include antibody-antigen interactions, enzyme-substrateinteractions, formation of duplexes or triplexes among polynucleotidesand/or oligonucleotides, receptor-ligand interactions, and the like. Asused herein, “contact” in reference to specificity or specific bindingmeans two molecules are close enough that weak noncovalent chemicalinteractions, such as Van der Waal forces, hydrogen bonding,base-stacking interactions, ionic and hydrophobic interactions, and thelike, dominate the interaction of the molecules.

As used herein, the term “T_(m)” is used in reference to the “meltingtemperature.” The melting temperature is the temperature (as measured in° C.) at which a population of double-stranded nucleic acid moleculesbecomes half dissociated into single strands. Several equations forcalculating the Tm of nucleic acids are well known in the art. Asindicated by standard references, a simple estimate of the Tm value indegrees Celsius may be calculated by the equation, Tm=81.5+0.41 (% G+C),when a nucleic acid is in aqueous solution at 1 M NaCl (see e.g.,Anderson and Young, Quantitative Filter Hybridization, in Nucleic AcidHybridization (1985). Other references (e.g., Allawi, H. T. &SantaLucia, J., Jr., Biochemistry 36, 10581-94 (1997)) includealternative methods of computation which take structural andenvironmental, as well as sequence characteristics into account for thecalculation of Tm.

“Sample” means a quantity of material from a biological, environmental,medical, or patient source in which detection, measurement, or labelingof target nucleic acids is sought. On the one hand it is meant toinclude a specimen or culture (e.g., microbiological cultures). On theother hand, it is meant to include both biological and environmentalsamples. A sample may include a specimen of synthetic origin. Biologicalsamples may be animal, including human, fluid, solid (e.g., stool) ortissue, as well as liquid and solid food and feed products andingredients such as dairy items, vegetables, meat and meat by-products,and waste. Biological samples may include materials taken from a patientincluding, but not limited to cultures, blood, saliva, cerebral spinalfluid, pleural fluid, milk, lymph, sputum, semen, needle aspirates, andthe like. Biological samples may be obtained from all of the variousfamilies of domestic animals, as well as feral or wild animals,including, but not limited to, such animals as ungulates, bear, fish,rodents, etc. Environmental samples include environmental material suchas surface matter, soil, water and industrial samples, as well assamples obtained from food and dairy processing instruments, apparatus,equipment, utensils, disposable and non-disposable items. These examplesare not to be construed as limiting the sample types applicable to thepresent invention.

The terms “upstream” and “downstream” in describing nucleic acidmolecule orientation and/or polymerization are used herein as understoodby one of skill in the art. As such, “downstream” generally meansproceeding in the 5′ to 3′ direction, i.e., the direction in which anucleotide polymerase normally extends a sequence, and “upstream”generally means the converse. For example, a first primer thathybridizes “upstream” of a second primer on the same target nucleic acidmolecule is located on the 5′ side of the second primer (and thusnucleic acid polymerization from the first primer proceeds towards thesecond primer).

It is further noted that the claims may be drafted to exclude anyoptional element. As such, this statement is intended to serve asantecedent basis for use of such exclusive terminology as “solely”,“only” and the like in connection with the recitation of claim elements,or the use of a “negative” limitation.

DETAILED DESCRIPTION OF THE INVENTION

The invention is drawn to asymmetrically tagging one or more nucleicacids in a sample using asymmetric adapters.

Before the present invention is described, it is to be understood thatthis invention is not limited to particular embodiments described, assuch may, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassedwithin the invention. The upper and lower limits of these smaller rangesmay independently be included or excluded in the range, and each rangewhere either, neither or both limits are included in the smaller rangesis also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either or both of those includedlimits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, some potential andpreferred methods and materials are now described. All publicationsmentioned herein are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. It is understood that the present disclosuresupersedes any disclosure of an incorporated publication to the extentthere is a contradiction.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “anucleic acid” includes a plurality of such nucleic acids and referenceto “the compound” includes reference to one or more compounds andequivalents thereof known to those skilled in the art, and so forth.

The practice of the present invention may employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such conventional techniques includepolymer array synthesis, hybridization, ligation, and detection ofhybridization using a label. Specific illustrations of suitabletechniques can be had by reference to the example herein below. However,other equivalent conventional procedures can, of course, also be used.Such conventional techniques and descriptions can be found in standardlaboratory manuals such as Genome Analysis: A Laboratory Manual Series(Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A LaboratoryManual, PCR Primer: A Laboratory Manual, and Molecular Cloning: ALaboratory Manual (all from Cold Spring Harbor Laboratory Press),Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York, Gait,“Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press,London, Nelson and Cox (2000), Lehninger, A., Principles of Biochemistry3^(rd) Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al. (2002)Biochemistry, 5^(th) Ed., W. H. Freeman Pub., New York, N.Y., all ofwhich are herein incorporated in their entirety by reference for allpurposes.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

As summarized above, the present invention provides methods andcompositions for asymmetrically tagging a nucleic acid fragment usingasymmetric adapters.

Methods of Asymmetrically Tagging a Nucleic Acid Fragment

Starting Nucleic Acids

Nucleic acids in a nucleic acid sample being analyzed (or processed) inaccordance with the present invention can be from any nucleic acidsource. As such, nucleic acids in a nucleic acid sample can be fromvirtually any nucleic acid source, including but not limited to genomicDNA, complementary DNA (cDNA), RNA (e.g., messenger RNA, ribosomal RNA,short interfering RNA, microRNA, etc.), plasmid DNA, mitochondrial DNA,etc. Furthermore, as any organism can be used as a source of nucleicacids to be processed in accordance with the present invention, nolimitation in that regard is intended. Exemplary organisms include, butare not limited to, plants, animals (e.g., reptiles, mammals, insects,worms, fish, etc.), bacteria, fungi (e.g., yeast), viruses, etc. Incertain embodiments, the nucleic acids in the nucleic acid sample arederived from a mammal, where in certain embodiments the mammal is ahuman.

In certain embodiments, the nucleic acids in the nucleic acid sample areenriched prior to analysis. By enriched is meant that the nucleic acidis subjected to a process that reduces the complexity of the nucleicacids, generally by increasing the relative concentration of particularnucleic acid species in the sample (e.g., having a specific locus ofinterest, including a specific nucleic acid sequence, lacking a locus orsequence, being within a specific size range, etc.). There are a widevariety of ways to enrich nucleic acids having a specificcharacteristic(s) or sequence, and as such any convenient method toaccomplish this may be employed.

In certain embodiments, nucleic acids in the nucleic acid sample areamplified prior to analysis. In certain of these embodiments, theamplification reaction also serves to enrich a starting nucleic acidsample for the locus of interest. For example, a starting nucleic acidsample can be subjected to a polymerase chain reaction (PCR) thatamplifies one or more region of interest. In certain embodiments, theamplification reaction is an exponential amplification reaction whereasin certain other embodiments, the amplification reaction is a linearamplification reaction. Any convenient method for performingamplification reactions on a starting nucleic acid sample can be used inpracticing the subject invention. In certain embodiments, the nucleicacid polymerase employed in the amplification reaction is a polymerasethat has proofreading capability (e.g., phi29 DNA Polymerase,Thermococcus litoralis DNA polymerase, Pyrococcus furiosus DNApolymerase, etc.).

In certain embodiments, the nucleic acid sample being analyzed isderived from a single source (e.g., a single organism, tissue, cell,subject, etc.), whereas in other embodiments, the nucleic acid sample isa pool of nucleic acids extracted from a plurality of sources (e.g., apool of nucleic acids from a plurality of organisms, tissues, cells,subjects, etc.), where by “plurality” is meant two or more. As such, incertain embodiments, a nucleic acid sample can contain nucleic acidsfrom 2 or more sources, 3 or more sources, 5 or more sources, 10 or moresources, 50 or more sources, 100 or more sources, 500 or more sources,1000 or more sources, 5000 or more sources, up to and including about10,000 or more sources. As described above, the nucleic acids in nucleicacid samples from a single source as well as from multiple sourcesinclude a locus of interest for which at least one reference sequence isknown.

In certain embodiments, nucleic acid fragments tagged according toaspects of the subject invention are to be pooled with nucleic acidfragments derived from a plurality of sources (e.g., a plurality oforganisms, tissues, cells, subjects, etc.), where by “plurality” ismeant two or more. In such embodiments, the asymmetric adapter employedfor each separate nucleic acid sample may include a uniquely identifyingtag (UID) such that after the tagging process is complete, the sourcefrom which the each tagged nucleic acid fragment was derived can bedetermined. Any type of UID can be used, including but not limited tothose described in co-pending U.S. patent application Ser. No.11/656,746, filed on Jan. 22, 2007, and titled “Nucleic Acid AnalysisUsing Sequence Tokens”, as well as U.S. Pat. No. 7,393,665, issued onJul. 1, 2008, and titled “Methods and Compositions for Tagging andIdentifying Polynucleotides”, both of which are incorporated herein byreference in their entirety for their description of nucleic acid tagsand their use in identifying polynucleotides. In certain embodiments, aset of UIDs employed to tag a plurality of samples need not have anyparticular common property (e.g., T_(m), length, base composition,etc.), as the asymmetric tagging methods (and many tag readout methods,including but not limited to sequencing of the tag or measuring thelength of the tag) can accommodate a wide variety of unique UID sets.

Asymmetric Adapter

Asymmetric adapters that find use in the present invention may have avariety of structural configurations, examples of which are describedbelow.

1. Asymmetric Adapters Having a Region of SubstantialNon-Complementarity

In certain embodiments, an asymmetric adapter includes one or more clampregions, a ligation site and a region of substantial non-complementaritysuch that when a asymmetric adapter is ligated to both ends of a nucleicacid fragment and the adapter-ligated fragment is amplified (orreplicated) through the region of non-complementarity, the resultantnucleic acid fragments are tagged asymmetrically, i.e., the nucleic acidfragment(s) produced have a different tag sequence on each end. Bydifferent tag sequence on each end is meant that a tag sequence on oneend of a nucleic acid fragment produced according to methods of thepresent invention has at least one region or domain that has a nucleicacid sequence that is different from a tag sequence on the other end.Embodiments of each of these features will be described in furtherdetail below.

FIG. 1 shows three embodiments for asymmetric adapter structures thatfind use in the present invention. The asymmetric adapter in FIG. 1Aincludes two nucleic acid strands: a top strand having elements 112 and106 in a 5′ to 3′ orientation, and a bottom strand having elements 114,108 and 110 in a 3′ to 5′ orientation. As is evident from the structureshown in FIG. 1A, elements 106 and 108 hybridize to one another forminga first clamp region that, when ligated to a compatible end of a nucleicacid fragment via ligation site 110 (discussed below), is proximal tothe nucleic acid fragment (also referred to as “inner”). As such, thesequence of element 106 is complementary to the sequence of element 108.The asymmetric adapter in FIG. 1B also includes two nucleic acidstrands: a top strand having elements 102, 112, and 106 in a 5′ to 3′orientation, and a bottom strand having elements 104, 114, 108, and 110in a 3′ to 5′ orientation. As with the structure shown in FIG. 1A,elements 106 and 108 in FIG. 1B hybridize to one another forming a firstclamp region that is proximal to the nucleic acid fragment once ligatedthereto (also referred to as “inner”). Unlike the asymmetric adapter inFIG. 1A, the asymmetric adapter in FIG. 1B includes elements 102 and 104which hybridize to one another forming a second clamp region that isdistal to the nucleic acid fragment (also referred to as “outer”). Assuch, the sequence of element 102 is complementary to the sequence ofelement 104 and the sequence of element 106 is complementary to thesequence of element 108. The length of such complementary regions whichform clamp structures in the asymmetric adapters can vary and, incertain embodiments, can be affected by other sequences in theasymmetric adapter, e.g., the region of substantial non-complementarity.In certain embodiments the length of the complementary sequence is from6 nucleotides to 50 nucleotides. For example, predictions based on a2-state hybridization model indicate that 6 bases of complementarity(having the sequence 5′ CTCCTC 3′ on the top strand) would be sufficientto form a proximal camp region under the following conditions: 50 mMNaCl, 10 mM MgCl₂, 10 uM adapter at 20° C.

The asymmetric adapter shown in FIG. 1C is similar to the one in FIG. 1Bexcept that rather than the second clamp region being formed from ahybridization region between the top and bottom strands, a cleavablelinker 116 is used to join the 5′ end of the top strand with the 3′ endof the bottom strand. In embodiments that employ an asymmetric adapterwith a cleavable linker as the distal clamp region, the cleavable linkeris cleaved prior to any subsequent extension steps performed on theasymmetric adapter tagged fragments (see description of exemplary methodbelow). Any convenient cleavable linker can be employed, includingnucleic acid, peptide or other chemical linkers that are uniquelysensitive to a cleaving agent. By uniquely sensitive is meant that onlythe cleavable linker (or specific region or chemical bond in thecleavable linker) is cleaved when a asymmetric adapter ligated nucleicacid fragment is contacted to the cleaving agent. For example, acleavable linker that includes ribonucleic acids can be cleaved bycontacting an asymmetric adapter ligated DNA fragment to RNase I. Asanother example, a cleavable linker that includes a disulfide bond canbe cleaved by contacting a asymmetric adapter ligated DNA fragment to areducing agent such as dithiothreitol.

The asymmetric adapter structures in FIGS. 1A, 1B and 1C include one ormore region of substantial non-complementarity represented by elements112 and 114 (denoted as regions α and β, respectively). This region isalso referred to herein as the “asymmetric” region. By substantiallynon-complementary is meant that one or both of elements 112 and 114include at least one region of nucleic acid sequence that is notcomplementary to the other strand, where in certain embodiments theasymmetric adapter includes 2, 3, 4, 5, or 6 or more regions ofnon-complementarity. The length and identity of the one or more regionof non-complementarity will vary based on the desires of the user (e.g.,based on the downstream analyses to be performed on the resultantasymmetrically tagged nucleic acid). For example, in certainembodiments, elements 112 and 114 (or α and β) include one or moreparticular sequences which are useful for later steps in the workflow.Such sequences include, but are not limited to, restriction enzymesites, PCR primer binding sites, linear amplification primer sites,reverse transcription primer sites, RNA polymerase promoter sites (suchas for T7, T3 or SP6 RNA polymerase), UID tags (e.g., tags employed tomark the nucleic acid fragment as being derived from a specific startingsample), sequencing primer sites, etc.

It is noted here that the UID tag need only be a DNA sequence whichuniquely identifies the sample or sample region from which the fragmentso labeled originates. It is noted here that there are no constraintswith regard to members of a set of tags being employed in the presentinvention. For example, a set of identity tags that finds use in thesubject invention need not have similar thermodynamic or physicalproperties between them, e.g., be isothermal.

As indicated above, the asymmetric adapters include a ligation site 110that is adjacent to the first, proximal clamp region (formed by 106 and108). The ligation site comprises a region of single-strandedness thatselectively associates with a compatible end of the nucleic acidfragments. The compatible region of single-strandedness may be on thebottom strand, forming a 5′ overhang (as shown in FIG. 1) or, in certainembodiments, be present on the top strand, forming a 3′ overhang. Inorder to promote ligation of the asymmetric adapter to a compatiblenucleic acid fragment, the 5′ end of the ligation site is phosphorylated(not shown in FIG. 1). Therefore, as described above and shown in FIG.1, the ligation site is configured to allow ligation of a asymmetricadapter to a compatible end of a nucleic acid fragment which is to beasymmetrically tagged.

In certain embodiments, compatible ends of a nucleic acid fragment areproduced by contacting a parent nucleic acid sample with a restrictionenzyme and polishing the ends (e.g., by adding a single base). As such,in these embodiments, the restriction enzyme generates nucleic acidfragments having cut sites on the ends that are compatible to the singlestranded region of the asymmetric adapter, i.e., the ends of the nucleicacid fragments have regions of complementarity to the region ofsingle-strandedness (i.e., the overhang regions at the cut site) in theligation site of the asymmetric adapter. In this way, the asymmetricadapter ligation site and compatible ends of the nucleic acid fragmentscan be ligated to one another under appropriate ligation conditions(e.g., in the presence of an enzyme having DNA ligase activity inappropriate buffering conditions and co-factors). See, e.g., FIG. 3,described in detail below.

In certain embodiments, compatible ends of the nucleic acid fragmentsare not produced by restriction enzyme digestion. For example, aparental nucleic acid sample can be fragmented by applying shear forcesto the sample, which leads to fragmented DNA. Polishing of the ends ofsuch fragmented DNA can then be performed to produce blunt ends havingno 5′ or 3′ overhang (e.g., by filling in and or removing overhangs asis known in the art). Asymmetric adapters compatible with such blunt-endfragments will themselves be blunt ended at the ligation site and have a5′ phosphate group. In these embodiments, the blunt ends of thefragmented nucleic acid are de-phosphorylated to prevent inter-fragmentligation.

In certain other embodiments, a blunt end nucleic acid fragment(s),whether produced by shearing or by a restriction enzyme the producedblunt ends, is contacted with a DNA polymerase that can add a singlespecific nucleotide in a non-template dependent manner (e.g., an addeddA to the 3′ end of blunt fragment using Taq polymerase). The compatibleasymmetric adapter in such embodiments will be designed to have acompatible end containing a single base overhang that is complementaryto the nucleotide added to the blunt ends of the fragment (e.g., theasymmetric adapter ligation site will have a 3′ dT overhang). Thisembodiment is akin to TA cloning systems employed for cloning Taqpolymerase produced PCR products.

As is clear from the description above, any convenient method forcreating compatible ends between nucleic acid fragments and asymmetricadapters to promote ligation of the asymmetric adapter while reducinginter-fragment ligation may be used.

FIG. 2 shows the secondary and domain structure of an exemplaryasymmetric adapter that finds use in aspects of the present invention.The asymmetric adapter in FIG. 2 includes two strands of DNA thatassociate to form two clamp regions, the first of which is formed bycomplementary sequences 108 and 106 and the second of which is formed bycomplementary sequences 102 and 104 (with the element numberscorresponding to those in FIG. 1). The asymmetric also includes aligation site 110 and a region of substantial non-complementarity (112and 114). Within this region of substantial non-complementarity (orasymmetric region), the asymmetric adapter includes a number of specificelements that are useful for downstream analyses. These include: anidentify tag region 202; sequencing primer sites A and B (204 and 206,respectively; e.g., for use in Roche 454 sequencing method); and a T7promoter region 208. As indicated above, virtually any functional domainor sequence of interest can be included in the region of substantialnon-complementarity, which, in general, will be determined by a userbased on the downstream assay(s) to be performed on the resultantasymmetrically tagged nucleic acid fragment.

As can be seen in FIG. 2, the region of substantial non-complementaritymay have small sub-domains in which duplex DNA forms. For example, in T7promoter region 208, there is a stretch of three bases 210 that form aduplex between the strands. As such, while in certain exemplary diagramsthe region of substantial non-complementarity (the asymmetric region) isshown as having no nucleic acid duplex structures, in certainembodiments, some nucleic acid duplex structures will form.

FIG. 3 shows steps in an exemplary method for asymmetrically tagging anucleic acid fragment according to aspects of the subject invention.

In this exemplary method, a parent nucleic acid sample containingstarting nucleic acid (e.g., genomic DNA) is digested in step 302 with arestriction enzyme (in this case BstYI) producing 5′ overhang GATC(BstYI has a recognition site of R/GATCY, where R is a purine and Y is apyrimidine as conventionally denoted in the art and the slash indicatingthe position of the cut site). At step 304, the 5′ GATC overhang isfilled in with dG on the bottom strand (shown as “g”), producing a 5′GAT overhang. This overhang represents the compatible end of the nucleicacid fragment that will serve as a ligation site for a suitably designedasymmetric adapter (i.e., one having a 5′ ATC overhang). The fill-instep 304 prevents the restriction-digested, double-stranded fragments ofthe starting nucleic acid sample from being ligated to each other duringthe asymmetric adapter ligation step (i.e., prevents inter-fragmentligation).

It is noted here that there are numerous ways in which to producenucleic acid fragments having ends compatible with an asymmetricadapter. Producing compatible ends may include, but is not limited to,cutting with a restriction enzyme, shearing the nucleic acid, adding oneor more nucleotides, removing one or more nucleotides, and adding orremoving a phosphate group. The process of generating compatible ends ona nucleic acid fragment is sometimes referred to herein as “polishing”.The resultant compatible ends can have blunt or sticky ends (i.e.,having compatible overhang regions), both terms being well known in theart.

In certain embodiments, a nucleic acid fragment may be ligated to twoindependent and distinct asymmetric adapters, each of which is ligatedto a different compatible end of a nucleic acid fragment. Any convenientmethod for producing a nucleic acid fragment(s) having more than onedistinct compatible end can be employed. In certain of theseembodiments, the different compatible ends of the nucleic acid fragmentare produced by digesting the nucleic acid fragment with more than onerestriction enzyme. These multiply-digested fragments are ligated toseparate asymmetric adapters, each of which will ligate to one of thecompatible ends. The ligation of these asymmetric adapters can besequential or simultaneous. In addition, more than two asymmetricadapters may be used to tag a nucleic acid sample containing multiplefragments with any variety of different compatible ends. This willdepend on the desires of the user and the specific analyses to beperformed on the resultant asymmetrically tagged nucleic acid fragments.

In step 306, asymmetric adapter 314 having 5′ATC overhang (shown in thebox) is ligated to the nucleic acid fragments having compatible 5′GAToverhangs on both ends. The asymmetric adapters shown include two clampregions 316 (proximal and distal, with respect to their positionrelative to the nucleic acid fragment once ligated to it) formed bycompatible ends of the two strands of the asymmetric adapter. The topstrand of the asymmetric adapter includes a region of substantialnon-complementarity designated as α and the bottom strand of theasymmetric includes a region of substantial non-complementaritydesignated as β. In other words, α and β are not fully complementarysequences, and as such do not form a continuous hybridized structure. Asdescribed above, regions α and β may include specific regions thatfacilitate or allow specific downstream analyses as desired by a user ofthe method.

In step 308, the adapter ligated nucleic acid fragment(s) is moderatelydenatured in the asymmetric region and a synthesis primer 310 isannealed in the β region. Only the bottom strand of the asymmetricadapter ligated nucleic acid fragment is shown here. In certainembodiments, the β region in the top strand will also have an annealedprimer 310 in the β region.

Once annealed, the synthesis primer is extended by contacting theasymmetric adapter tagged nucleic acid fragment with a nucleotidepolymerase under nucleic acid polymerizing conditions to produce anasymmetrically tagged nucleic acid fragment in step 312. Specifically,the resultant nucleic acid fragment includes a β region and itscomplement [β (comp) in FIG. 3] (or a substantial portion of the βregion, depending on where the synthesis primer 310 binding site islocated) on one end and an β region and its complement [α (comp) in FIG.3] on the other. In certain embodiments, the extension reaction is alinear amplification reaction while in other embodiments the extensionis an exponential amplification reaction (e.g., a conventional PCRreaction). Any convenient method for extending/amplifying the asymmetricadapter tagged nucleic acid fragment that will produce an asymmetricallytagged nucleic acid can be employed, including DNA polymerization or RNApolymerization.

Once extended, the now asymmetrically tagged nucleic acid fragment canbe manipulated and assayed as desired by the user. As noted above,functional regions or domains in the substantially non-complementaryregions of the asymmetric adapter can facilitate such downstreamanalyses (e.g., sequencing, amplification, sorting based on an identitytag, etc.).

In certain embodiments, the method may include isolating only one strandof an asymmetric adapter ligated nucleic acid fragment, and as such,only one strand will be processed in downstream steps. For example, onecan treat the asymmetrically tagged DNA shown on the bottom of FIG. 3with Exonuclease III to remove the top strand of the duplex. As is wellknow in the art, Exonuclease III catalyzes the stepwise removal ofmononucleotides from 3′-hydroxyl termini of double-stranded DNA. Due tothe location of priming of synthesis primer 310 (i.e., in the β region,which is several bases in from the 3′ end of the template strand), theasymmetrically tagged duplex DNA at the bottom of FIG. 3 has a 3′ singlestranded overhang on the left side but not on the right side. BecauseExonuclease III will only digest double stranded DNA in the 3′ to 5′direction, only the top strand is sensitive to this enzyme, withdigestion proceeding from the right side (i.e., from the “α complement”side).

As another example, T7 exonuclease can be employed to remove the bottomstrand of the asymmetrically tagged DNA shown at the bottom of FIG. 3.As is known in the art, T7 exonuclease catalyzes the removal of 5′mononucleotides from double-stranded DNA in the 5′ to 3′ direction. Ifsynthesis primer 310 is designed to incorporate a T7 exonucleaseblocking moiety (e.g., three or more phosphorothioate linkages), theactivity of T7 exonuclease can be blocked from the left side of theadapter-ligated fragment. The right side of the adapter-ligatedfragment, however, does not include the T7 exonuclease blocking moietyin element 102 of the adapter, and thus is sensitive to the 5′ to 3′exonuclease activity of T7 exonuclease. Thus, only the bottom strand issensitive to this enzyme, with digestion proceeding from the right side(i.e., from the “α” side). Conversely, the top strand can be removedwith T7 exonuclease if element 102 of the adapter includes a T7exonuclease blocking moiety (element 102 is the same as shown in FIG.1B).

In other embodiments, Lambda Exonuclease can be used to remove onestrand of an adapter ligated fragment. As is known in the art, LambdaExonuclease catalyzes the removal of 5′ mononucleotides from5′-phosphorylated double-stranded DNA. Thus, including a 5′ phosphate onthe 5′ end of the outer region of the adapter (i.e., on the 5′ end of102), only the bottom strand of the adapter ligated fragment shown onthe bottom of FIG. 3 will be degraded, leaving the top strand intact. Toremove the top strand of this adapter ligated fragment with lambdaexonuclease, synthesis primer 310 can include a 5′ phosphate. Thephosphorylation of either the asymmetric adapter or the synthesis primer310 can be done synthetically or enzymatically (e.g., with T4polynucleotide kinase).

In certain other embodiments, primer 310 includes a member of a bindingpair, e.g., a biotin moiety at its 5′ end, which can be used toimmobilize the top strand on a streptavidin moiety bound to a solidsupport. Removal of the hybridized, non-biotinylated strand (the bottomstrand) by denaturation using heat or high pH serves to isolate thebiotinylated top strand.

The implementation of a single strand isolation step using the methodsdescribed above or variations thereof (or any other convenient singlestrand isolation step) will generally be based on the desires of theuser.

FIG. 4 shows an exemplary tagged nucleic acid fragment in which theasymmetric adapter contains certain specific functional regions. FIG. 4shows a genomic fragment (GF strand and complementary GF′ strand)ligated to an asymmetric adapter at both ends, where the asymmetricadapter contains a number of specific functional elements and regions.As shown, the adapter contains an outer clamp region (OCR) and an innerclamp region (ICR) with an asymmetric region there-between. One strandof this asymmetric region includes a sequencing primer binding site fornext generation sequencing (454B element; used in the Roche 454sequencing system), while, the other strand of this asymmetric regionincludes a sequence complementary to a second sequencing primer bindingsite (454A′; also used in the Roche 454 sequencing system), a sequencecomplementary to a T7 promoter site (T7′), and a sequence complementaryto a UID tag (UID′; the “prime” symbol in this figure indicates a regionthat is complementary to the noted functional region of interest).

Replication of this asymmetrically-tagged genome fragment with a T7primer results in the two different double stranded fragments: the firstof which represents replication of the top strand of the adapter ligatedfragment and the second of which represents replication of the bottomstrand of the adapter ligated fragment (the bottom strand replicationproduct is shown in reverse orientation). As can be seen in FIG. 4, thereplication of asymmetrically tagged genome fragments produces productshaving both orientations of the genomic fragment with respect to thetags on the end. This is illustrated in FIG. 4B by the a to zorientation of the GF/GF′ regions.

FIG. 5 shows another exemplary embodiment of an asymmetric adapteraccording to aspects of the present invention. This adapter is similarto the “Y” adapter as shown in FIG. 1A but includes a hairpin structureon the 3′ end of the asymmetric region (i.e., opposite end from theligation site). This hairpin structure allows for self-priming of thefirst round of replication from the 3′ end (e.g., by a DNA polymerase),forming double-stranded products having a hairpin at one end (notshown). This hairpin structure can be exploited for further downstreamprocess steps, including in amplification of the resultant taggedfragments. As discussed in detail above, asymmetric adapters can includeany number of additional functional elements. As but one example, theinclusion of a T7 promoter site oriented such that RNA polymerizationproceeds in the direction of the hairpin (“T7”, as shown in FIG. 5,where the arrow indicates the direction of RNA polymerization) allowsfor specific isothermal amplification processes to be carried, e.g., asdescribed in detail in U.S. patent application Ser. No. 11/338,533 filedon Jan. 23, 2006 entitled “Isothermal DNA Amplification”, incorporatedby reference herein in its entirety. It is noted that the T7 promotersite may be present in the hairpin structure of the adapter as shown inFIG. 5 or in the single-stranded portion of the β region (as replicationfrom the self-priming site will reconstitute a fully functional T7promoter). Although not shown in FIG. 5, asymmetric adapters having ahairpin structure at the 3′ end opposite the ligation site may includemore than one clamp region (e.g., an asymmetric adapter as shown in FIG.1B with the addition of a 3′ hairpin on the end opposite the ligationsite).

2. Asymmetric Adapters Having Wobble Bases

In certain embodiments, an asymmetric adapter includes a ligation site(as described in detail above) and one or more wobble base. By “wobblebase” is meant a nucleic acid base that can base pair with a firstnucleotide base in a complementary nucleic acid strand but that, whenemployed as a template strand for nucleic acid synthesis, leads to theincorporation of a second, different nucleotide base into thesynthesizing strand. Non-limiting examples of such wobble bases include:8-oxo-dA, which can base pair with dG in a complementary strand but willlead to the incorporation of dT at the corresponding position when usedas a template for nucleic acid synthesis; 8-oxo-dG, which can base pairwith dA in a complementary strand but will lead to the incorporation ofdC at the corresponding position when used as a template for nucleicacid synthesis; and deoxy-inosine (dI), which can base pair with any ofdG, dA, dC or dT (or dN) in a complementary strand but will lead to theincorporation of dC at the corresponding position when used as atemplate for nucleic acid synthesis. Any convenient wobble base may beused in the adapters of the present invention.

The presence of one or more wobble base in an asymmetric adapter allowsthe production of asymmetrically tagged nucleic acids after a firstround of nucleic acid synthesis. This basic concept is shown in FIG. 6,where the asymmetric adapter is shown in 6A. In this exemplaryasymmetric adapter, I represents inosine, A* represents 8-oxo-dA and G*represent 8-oxo-dG. While this exemplary adapter has all of the wobblebases in the bottom strand, any configuration of wobble bases may beused, including one or more wobble bases in the top strand, in thebottom strand (as shown) or in both the top and bottom strand. Thenumber, type and position of wobble bases in an asymmetric adapter willdepend on the desires of the user and generally will be based ondownstream steps and analyses to be performed. Also indicated in thisadapter are a nucleic acid synthesis primer binding site and a ligationsite, both of which have been described in detail above.

FIG. 6B shows the asymmetric adapter in 6A attached to both ends of anucleic acid fragment (denoted as “insert” in this figure) and theresultant replicated product produced by nucleic acid synthesis from aprimer that binds to the primer binding site of the asymmetric adapter(primers shown as arrows). The resultant nucleic acid synthesis productshown is only for replication of the top strand of the asymmetricadapter-ligated fragment. As can be seen in FIG. 6B, the left endadapter of the replicated top strand now includes the sequence: 5′-G A TG T A A A G-3′ while the corresponding sequence in the right end adapterhas the sequence: 5′-C C T T T C A C G-3′. This fragment is thusasymmetrically labeled.

In certain embodiments, the primer employed for nucleic acid synthesisis modified such that it can be used to purify the replicated strand(the strand having asymmetric adapters) from the original templatestrand (e.g., the primer may include a binding moiety, e.g., a biotin,which can be purified using a corresponding binding partner, e.g.,streptavidin, as discussed above). In certain other embodiments, thesynthesis primer is immobilized on a solid substrate, thereby producinga solid support bound replication product.

The wobble base (or bases) may be present one or more specific elementsof the asymmetric adapter, including, but not limited to, promoterregions, primer binding sites, restriction enzyme recognition/cut sites,ligation sites, UID tags, etc.

In certain embodiments, at least one wobble base (or bases) is presentin a restriction enzyme recognition/cut site in the asymmetric adaptersuch that upon replication, a functional restriction enzyme cut sitewill be present on only one side of the asymmetrically labeled fragment.An exemplary embodiment is shown in FIG. 6C, where this embodiment isgenerally employed for inserts that do not include a Cla I site (e.g.,where the restriction enzyme Cla I is used to fragment the genomic DNA).In this embodiment, the restriction site Cla I is present in the topstrand of the adapter with wobble bases I (inosine), 8-oxo-dA (A*) and8-oxo-dG (G*) present in the bottom strand. Positions of the synthesisprimer binding site and the ligation site are also indicated. Afterligation to a fragment and one round of replication using acorresponding synthesis primer (arrow) (FIG. 6D), the Cla I site ispreserved in the adapter on the left side of the replicated fragmentshown (the replicated top strand) but is lost in the adapter on theright side of the fragment. The presence of an asymmetric restrictionenzyme site allows for a variety of unique manipulations of the taggedfragment. For example, the restriction site can be employed as a site toplace a second adapter onto the fragment, where this second adapterincludes sequences not present in the first adapter. Specifically,asymmetrically tagged fragments having a restriction site present ononly one end can be cleaved with the restriction enzyme (e.g., Cla I asshow in FIG. 6D) followed by ligation of a complementary, second adapterat this site. As discussed above in the example employing BstYIrestriction sites, a single nucleotide fill-in reaction may also besimilarly employed prior to the ligation of the second adapter toprevent undesirable ligation reactions between compatible fragment ends(with Cla I, which leaves 5′CG overhang, one could fill in with C andligate adapters having 5′G overhang).

In certain embodiments, rather than destruction of a restriction enzymesite present in an adapter as described above, a new restriction enzymesite can be created using wobble bases. For example, an adapter having atop strand containing the sequence 5′-A G G G A T-3′ paired with abottom strand having a corresponding sequence 5′-A T C I A* T-3′ (whereI is inosine and A* is 8-oxo dA) would reconstitute a ClaI siteasymmetrically after replication (not shown in the figures).

In certain embodiments, the wobble base is present in the ligation siteof the adapter. An exemplary embodiment is shown in FIG. 7. In thisfigure, DNA fragments are produced by digestion with BstYI followed by afill-in reaction with dGTP (added base shown in small letter “g” in FIG.7), which prevents fragment co-ligation in the subsequent ligationreaction (as described above). A generic fragment is shown at the top ofFIG. 7. An adapter that includes two wobble bases (denoted A* and G*,which are 8-oxo dA and 8-oxo dG, respectively) are then ligated to bothends of these fragments. A first round of replication theseadapter-fragment complexes using primers that prime in the adapterregion (shown as arrows) produces products in which the BstYIrestriction site is regenerated on only one end of the fragments (leftside as shown in the exemplary fragment in FIG. 7; note the absence of aBstYI site at the right end of the fragment). This asymmetricrestriction site can be used as a site for ligating a second, differentadapter if desired by digestion with BstYI, removal of the left endadapter (e.g., using a binding moiety scheme as described above, e.g.,where the synthesis primer is biotinylated facilitating removal of theleft-side adapter after BstYI digestion), and ligation of a second,different adapter having at least one region with a sequence differentthan the first adapter (and, e.g., where the ligation is performed aftera “g” fill in of the fragment as in the previous steps).

Kits and Systems

Also provided by the subject invention are kits and systems forpracticing the subject methods, as described above, such as one or moreasymmetric adapters, components to create compatible ends for theasymmetric adapters, and regents for generating the asymmetricallytagged fragments after asymmetric ligation (e.g., restriction enzymes,nucleotides, polymerases, primers, etc.). The various components of thekits may be present in separate containers or certain compatiblecomponents may be precombined into a single container, as desired.

The subject systems and kits may also include one or more other reagentsfor preparing or processing a nucleic acid sample according to thesubject methods. The reagents may include one or more matrices,solvents, sample preparation reagents, buffers, desalting reagents,enzymatic reagents, denaturing reagents, where calibration standardssuch as positive and negative controls may be provided as well. As such,the kits may include one or more containers such as vials or bottles,with each container containing a separate component for carrying out asample processing or preparing step and/or for carrying out one or moresteps of a nucleic acid variant isolation assay according to the presentinvention.

In addition to above-mentioned components, the subject kits typicallyfurther include instructions for using the components of the kit topractice the subject methods, e.g., to asymmetrically tag a nucleic acidfragment(s) according to aspects of the subject methods. Theinstructions for practicing the subject methods are generally recordedon a suitable recording medium. For example, the instructions may beprinted on a substrate, such as paper or plastic, etc. As such, theinstructions may be present in the kits as a package insert, in thelabeling of the container of the kit or components thereof (i.e.,associated with the packaging or sub-packaging) etc. In otherembodiments, the instructions are present as an electronic storage datafile present on a suitable computer readable storage medium, e.g.CD-ROM, diskette, etc. In yet other embodiments, the actual instructionsare not present in the kit, but means for obtaining the instructionsfrom a remote source, e.g. via the internet, are provided. An example ofthis embodiment is a kit that includes a web address where theinstructions can be viewed and/or from which the instructions can bedownloaded. As with the instructions, this means for obtaining theinstructions is recorded on a suitable substrate.

In addition to the subject database, programming and instructions, thekits may also include one or more control samples and reagents, e.g.,two or more control samples for use in testing the kit.

Utility

The asymmetric nucleic acid labeling method described herein enables oneto accomplish the asymmetric labeling of a nucleic acid fragment(s) ofinterest in only a few steps with high yield. This is a significantadvantage over asymmetric labeling method known in the art. Because thesubject invention finds use in any process or analysis for whichasymmetric fragment labeling is desired (e.g., assays in which one needsto control subsequent manipulations and reactions with respect to oneparticular strand of DNA) it will be applicable to a variety of nucleicacid analyses currently being performed (e.g., high throughputsequencing assays) as well as provide a catalyst for the development ofnovel assays that rely on the efficient asymmetric labeling of nucleicacids. Therefore, no limitation with regard to the types of assays towhich the subject invention may be applied is intended.

EXAMPLES Example I Asymmetric Adapter

The asymmetric adapter employed is shown in FIG. 8. The top and bottomstrand sequences of the asymmetric adapter are shown and include thefollowing structural features: clamp regions 402 and 404; regions ofsubstantial non-complementarity α (406) and β (408); and ligation site414. The bottom strand also includes a sequence 412 that iscomplementary to the T3 RNA promoter while the top strand includesreverse primer sequence 410. These two elements will be used in latersteps to confirm that the asymmetric adapter produces a library ofasymmetrically tagged nucleic acids (i.e., the T3 promoter is on one endand the reverse primer is on the other end of the resultantasymmetrically tagged nucleic acid fragments).

The asymmetric adapter in FIG. 8 is designed to be ligated to nucleicacid fragments having a 5′ GAT overhang (e.g., fragments cut with arestriction enzyme leaving a 5′GATC overhang followed by a fill-inreaction with dGTP, as shown in FIG. 3 and described above). The forwardprimer sequence which anneals to the underlined sequence to make T3promoter double stranded DNA is also shown in FIG. 8 (SEQ ID NO: 4;complement to underlined sequence 412). This forward primer, whenannealed to its target location in the asymmetric adapter, can be usedeither as a DNA synthesis primer to make double stranded DNA (e.g., asshown in FIG. 16A; e.g., for use in in vitro transcription (IVT)reactions) or as a double stranded T3 promoter site that can be useddirectly to produce an RNA copy of the top strand (e.g., as shown inFIG. 16C). The reverse primer, which can be used to make 1st strandedcDNA from an RNA copy of the adapter ligated fragment, is indicated inFIG. 8 (SEQ ID NO: 3; identical to underlined sequence 410).

FIG. 9 shows a predicted secondary structure of the asymmetric adapterin FIG. 8. Secondary structure of the asymmetric adapter was predictedby two-state hybridization model[http(colon)//dinamelt(dot)bioinfo(dot)rpi(dot)edu/twostate(dot)php]under the following conditions: 50 mM NaCl, 10 mM MgCl₂, 57° C., 10 uMadapter concentration. The dG and dH (often referred to as ‘delta G’ and‘delta H’ or ΔG and ΔH) values shown at the bottom of FIG. 9 arecomputed from this model.

Exonuclease sensitivity of the asymmetric adapter was checked in orderto confirm that the end structure of the adapter is double stranded. Inaddition, as the asymmetric adapter contains a large internal loop,accessibility of the ligation site 414 needed to be determined. FIG. 10shows results of single stranded DNA specific exonuclease Exonuclease Iand/or double stranded specific exonuclease lambda exonuclease treatmentof the asymmetric adapter. The top strand is denoted in FIG. 10 as R andthe bottom strand as T. The asymmetric adapter is thus formed byannealing strand R to strand T. As shown in this Figure, Exonuclease Idid not affect the adapter migration (lane 6) but lambda exonucleasedoes (lane 7). When both enzymes present, the asymmetric adapter isdegraded (lane 8). These Exonuclease sensitivity experiments confirmthat both ends of the asymmetric adapter are double stranded aspredicted.

Library Production

The asymmetric adapter described above was used to make a library ofasymmetrically tagged nucleic acid fragments. FIG. 11 shows a gelanalysis demonstrating successful asymmetric adapter libraryconstruction from lambda DNA digested with BstYI. Lanes 1 through 7demonstrate the importance of the single base fill-in reaction toprevent concatenation of the lambda fragments. Successful adapterligation on both ends of each fragment is confirmed (lane 15) by thedegradation sensitivity of Exonuclease I and lambda exonuclease. The 5′end of the distal side of the adapter (i.e., distal clamp region 402 asshown in FIG. 8) is lacking a phosphate group, which protects asymmetricadapter ligated DNA from lambda exonuclease degradation. Significantdegradation is observed after exonuclease treatment unless the adapteris ligated (lane 13).

In Vitro Transcription (IVT)

An in vitro transcription (IVT) reaction was performed directly from theadapter library obtained in FIG. 11. The library was denatured in mildconditions to avoid complete denaturation but enough denaturation toallow access of an antisense oligonucleotide that produces a doublestranded T3 promoter region (see the template shown in FIG. 15,described below). Lane 1 of FIG. 12 shows the template DNA (the samelambda library as studied in results shown in FIG. 11) for IVT; Lane 3shows the IVT pattern from the DNA template shown in Lane 1. Lanes 2 and4 show the template DNA treated with DNaseI or IVT reaction followed byDNaseI treatment, respectively. The proximal (5′ end) and distal (3′end) sequence of transcribed RNA is shown at the bottom of FIG. 12.These results show that the T3 promoter region is successfullyconstructed as double stranded form (by annealing the appropriateoligonucleotide probe) and the template is utilized for transcription byT3 RNA polymerase as predicted.

First Strand cDNA Synthesis.

In order to confirm the identity of the RNA transcript produced above,reverse primer priming ability was checked by the synthesis of a firststranded cDNA. As shown in FIG. 13, the transcript strand produced aboveshould contain the complementary sequence of reverse primer located nearthe 3′ end of the IVT transcript produced in the previous step. FIG. 13shows that cDNA was synthesized from the labeled reverse primer (Lanes 3and 4). The position of the reverse primer is underlined in the sequenceshown in FIG. 13 (primer designated by the arrow). This resultdemonstrates that the predicted strand was utilized for the IVT reactionas the transcript contains complementary sequence of the reverse primerat/near its 3′ end. FIG. 16C provides a diagram of the product of thereverse transcription shown in FIG. 13. It is important to note that theRT product shown in lane 4 of FIG. 13 was produced from theDNaseI-treated IVT product shown in lane 4 of FIG. 12. Because thesample was treated with DNaseI before the RT reaction was performed, thetemplate for the RT product shown in lane 4 of FIG. 13 can only be theIVT RNA produced in the IVT reaction from the asymmetrically taggedtemplate.

The size of specific synthesis products from the BstYI lambda libraryusing forward and reverse primers (as described above) were analyzed ona sequencing gel (a high resolution, denaturing polyacrylamide gel) tocheck the size distribution of each fragment (FIG. 14). Lane 1 of FIG.14 shows the product produced by annealing a labeled forward primer(primer 502 in FIG. 15) to the lambda DNA adapter library followed byextension with Bst DNA polymerase (the expected product is the topstrand shown in FIG. 16A). Lane 2 of FIG. 14 shows the product producedby annealing and extending (with Bst DNA polymerase) a labeled reverseprimer to an unlabeled product produced as described for Lane 1 (theexpected product is the bottom strand shown in FIG. 16B). Lane 3 of FIG.14 shows the product of first stranded cDNA synthesis using a labeledreverse primer in an RT reaction, where the template strand istranscribed RNA produced from the T3 promoter from fully double strandedDNA (the template for T3 RNA polymerase is shown in FIG. 16A; the RNAtemplate for the RT reaction is shown in the top strand of FIG. 16C; andthe expected product is shown in the bottom strand of FIG. 16C). Theexpected size difference (in terms of numbers of base pairs) of eachcorresponding fragment between the products in Lanes 1 and 2 of FIG. 14(also called Δ1/2) is 12 bases (Δ1/2=12), as the reverse primer primesat a site that is 12 nucleotides in from the end of the adapter (seebinding site for the reverse primer 512 in FIG. 16B). The sizedifference of each corresponding fragment between lanes 2 and 3 of FIG.14 (called Δ2/3) is 19 bases (Δ2/3=19), as the transcriptional startsite is 19 bases from the 5′ end of the forward primer, thus resultingin a template for the reverse primer that is 19 bases shorter than thetemplate produced using the forward primer as a DNA synthesis primer (aswas done for lane 2). The library fragment distribution observed in FIG.14, lanes 1 to 3, shows the expected migration pattern: each fragment inlane 2 is shifted 12 bases down from each corresponding fragment in lane1 and each fragment in lane 3 is sifted 19 bases down from eachcorresponding fragment in lane 2. These results indicate that initiationof transcription occurs from one side of the adapter ligated fragments(i.e., from the T3 promoter) while RT initiation is initiated on theother side of the adapter ligated fragments (i.e., from the reverseprimer binding site). Thus, the library produced is asymmetric withrespect to the adapters on the opposite ends of each fragment in thelibrary.

Lane 5 of FIG. 14 shows the first stranded cDNA from RNA transcribedfrom an annealed forward primer in the adapter (as shown in FIG. 15).First stranded cDNA distribution in lane 5 is identical to that of lane3, in which the RNA transcription template was fully double stranded DNA(as in FIG. 16C). However, the yield of 1st stranded cDNA is lower whenthe RNA is produced from the template shown in FIG. 15 (where thetemplate still has regions of non-complementarity on both ends) thanfrom the template shown in FIG. 16C (where the template has undergone atleast one round of nucleic acid synthesis and thus does not includethese non-complementary regions). This can be seen by comparing lanes 3and 5.

FIG. 15 shows a possible DNA template for IVT reactions. Small lettersbelong to insert DNA and capitals belong to adapter sequence.

The following elements are indicated: filled in dGTP 504; 3 basesnucleotide 5′ overhang ATC from adapter (ATC in box 506); distal clampregion 402 and proximal clamp region 404; annealed forward primer 502(the T3 promoter sequence is indicated by box 510); asymmetric regions α(406) and β (408); and reverse primer sequence 410. The single, boldline connecting the adapter structures represents the double strandednucleic acid fragment tagged with the asymmetric adapters (labeled“Double-stranded fragment”).

FIG. 16A shows an adapter ligated DNA (represented as in FIG. 15, andlabeled “Double-stranded fragment”) that has been annealed with primer502 of FIG. 15 (SEQ ID NO: 4) and extended by DNA polymerase. Thefollowing elements are indicated: filled in dGTP 504; 3 bases nucleotide5′ overhang ATC from adapter (ATC in box 506); distal clamp region 402and proximal clamp region 404 (underlined in bottom strand); forwardprimer region 502 with T3 promoter sequence in box 510. The lineconnecting the adapter structures represents the nucleic acid fragmenttagged with the asymmetric adapters. Original template DNA for primerextension is in the bottom strand. Small letters belong to the insertDNA, capitals belong to adapter sequence.

FIGS. 16B and 16C show extended sequences produced by reverse primerpolymerization using either DNA as template and a DNA polymerase (FIG.16B) or RNA as a template and a reverse transcriptase (FIG. 16C). Thereverse primer 512 is the same as element 410 shown in FIGS. 8 and 15(SEQ ID NO: 3).

Extended sequences from the reverse primer 512 in FIGS. 16B and 16C areshown on the bottom strand.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it is readily apparent to those of ordinary skill in theart in light of the teachings of this invention that certain changes andmodifications may be made thereto without departing from the spirit orscope of the appended claims.

Accordingly, the preceding merely illustrates the principles of theinvention. It will be appreciated that those skilled in the art will beable to devise various arrangements which, although not explicitlydescribed or shown herein, embody the principles of the invention andare included within its spirit and scope. Furthermore, all examples andconditional language recited herein are principally intended to aid thereader in understanding the principles of the invention and the conceptscontributed by the inventors to furthering the art, and are to beconstrued as being without limitation to such specifically recitedexamples and conditions. Moreover, all statements herein recitingprinciples, aspects, and embodiments of the invention as well asspecific examples thereof, are intended to encompass both structural andfunctional equivalents thereof. Additionally, it is intended that suchequivalents include both currently known equivalents and equivalentsdeveloped in the future, i.e., any elements developed that perform thesame function, regardless of structure. The scope of the presentinvention, therefore, is not intended to be limited to the exemplaryembodiments shown and described herein, Rather, the scope and spirit ofpresent invention is embodied by the appended claims.

1. A method of producing an asymmetrically tagged nucleic acid fragment,said method comprising: i) ligating an adapter to each end of adouble-stranded nucleic acid fragment, wherein said adapter comprises:(a) a first and a second nucleic acid strand associated with each othervia one or more complementary domains, said adapter having a first endand a second end; (b) one or more region of substantialnon-complementarity between said first and second nucleic acid strands;(c) a ligation site positioned on said first end of said adapterconfigured to allow ligation of said adapter to said double strandednucleic acid fragment; and (d) a hairpin structure positioned on the 3′strand on said second end of said adaptor, said hairpin structureproducing a nucleic acid synthesis self-priming site; and ii) performinga first round of nucleic acid synthesis initiated from said self-primingsite using a nucleotide polymerase, thereby producing an asymmetricallytagged nucleic acid fragment.
 2. The method of claim 1, wherein saidnucleotide polymerase is selected from the group consisting of: a RNApolymerase, a mesophilic DNA polymerase, a reverse transcriptase, and athermophilic DNA polymerase.
 3. The method of claim 1, wherein in saidregion of substantial non-complementarity, said first and/or secondnucleic acid strands comprise one or more of the following: a uniqueidentifier (UID), an RNA polymerase promoter region, a primer bindingsite, a restriction enzyme site, and a recombination site.
 4. The methodof claim 1, wherein said adaptor comprises an RNA polymerase promoterregion adjacent to said hairpin structure or within the duplex region ofsaid hairpin structure.
 5. The method of claim 4, wherein said RNApromoter region is oriented such that RNA polymerization proceeds towardsaid hairpin structure.
 6. The method of claim 1, wherein saiddouble-stranded nucleic acid fragment is produced by digesting a parentdouble-stranded nucleic acid sample with a restriction enzyme andpolishing the ends of the resultant restriction enzyme fragments tocreate ends compatible with said ligation site of said adapter.
 7. Themethod of claim 1, wherein said method further comprises isolating onestrand of said asymmetrically tagged nucleic acid fragment.
 8. Themethod of claim 7, wherein said isolating comprises treating saidasymmetrically tagged nucleic acid fragment with an exonuclease selectedto digest only one strand of said asymmetrically tagged nucleic acidfragment.
 9. A nucleic acid adapter comprising: (a) a first and a secondnucleic acid strand associated with each other via one or morecomplementary domains, said adapter having a first end and a second end;(b) one or more region of substantial non-complementarity between saidfirst and second nucleic acid strands; (c) a ligation site positioned onsaid first end of said adapter configured to allow ligation of saidadapter to a double stranded nucleic acid fragment; and (d) a hairpinstructure positioned on the 3′ strand on said second end of saidadaptor, said hairpin structure producing a nucleic acid synthesisself-priming site.
 10. The adapter of claim 9, wherein said region ofsubstantial non-complementarity in said first or second nucleic acidstrand comprises one or more of the following: a unique identifier(UID), an RNA polymerase promoter region, a primer binding site, arestriction enzyme site, and a recombination site.
 11. The adapter ofclaim 9, wherein said adaptor comprises an RNA polymerase promoterregion adjacent to said hairpin structure or within the duplex region ofsaid hairpin structure.
 12. The method of claim 1, wherein said adaptercomprises one or more wobble base pair positioned in said one or morecomplementary domains such that said resultant asymmetrically taggednucleic acid fragment comprises a restriction enzyme recognition and/orcut site at only one end.
 13. The method of claim 12, wherein said oneor more wobble base pair is positioned within said ligation site. 14.The method of claim 12, wherein said method further comprises: digestingsaid asymmetrically tagged nucleic acid fragment with a restrictionenzyme specific for said restriction enzyme recognition and/or cut site;and ligating a second, different adapter to said digested fragment, saidsecond adapter having a ligation site compatible with the digested endof said fragment.
 15. The adapter of claim 9, wherein said adapterfurther comprises one or more wobble base pair positioned in said one ormore complementary domains within a restriction enzyme recognitionand/or cut site in said adapter.
 16. The method of claim 1, wherein saidadapter further comprises a cleavable linker in the loop region of saidhairpin structure.
 17. The adapter of claim 9, wherein said adapterfurther comprises a cleavable linker in the loop region of said hairpinstructure.